Average Number Of Alleles Research Articles

Utilizing SSR-based core collection development to improve conservation and utilization of Corylus L. genetic resources.

Hazelnuts are traditional woody oilseed plants. Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus L. germplasms using 16 simple sequence repeat (SSR) markers. Based on this, 11 pairs of core primers were selected, a fingerprint database of germplasm resources was constructed, and a primary core collection was screened. The results indicated that these tested Corylus L. germplasms exhibited a high level of genetic diversity, with an average number of alleles (Na) per locus of 14.5 and a polymorphic information content of 0.777. The phylogenetic relationships among various hazelnut cultivars were characterized by complexity, and they were delineated into four distinct groups facilitated by genetic distance analyses. An SSR fingerprint database for 331 Corylus L. germplasms was successfully constructed using the 11 obtained core SSR markers to increase the discrimination efficiency. Ultimately, 127 primary core accessions of Corylus L. were selected. The retention rate for the observed Na and MAF (the minor allele frequency) in the primary core germplasm constructed based on a sampling proportion of 38.36% was 100% and 94.7%, respectively. Shannon's information index (I) was highly consistent between the core and original germplasms, indicating that the core germplasm could fully represent the genetic diversity of the original germplasm. Additionally, the principal coordinate analysis of the selected primary core germplasm was essentially consistent with that of the entire original germplasm, further supporting the broad representativeness of the core germplasm. This study provided a basis for precisely identifying and efficiently utilizing Corylus L. accession.

Developmental and validation of a novel small and high-efficient panel of microhaplotypes for forensic genetics by the next generation sequencing

BackgroundIn the domain of forensic science, the application of kinship identification and mixture deconvolution techniques are of critical importance, providing robust scientific evidence for the resolution of complex cases. Microhaplotypes, as the emerging class of genetic markers, have been widely studied in forensics due to their high polymorphisms and excellent stability.Results and discussionIn this research, a novel and high-efficient panel integrating 33 microhaplotype loci along with a sex-determining locus was developed by the next generation sequencing technology. In addition, we also assessed its forensic utility and delved into its capacity for kinship analysis and mixture deconvolution. The average effective number of alleles (Ae) of the 33 microhaplotype loci in the Guizhou Han population was 6.06, and the Ae values of 30 loci were greater than 5. The cumulative power of discrimination and cumulative power of exclusion values of the novel panel in the Guizhou Han population were 1-5.6 × 10− 43 and 1-1.6 × 10− 15, respectively. In the simulated kinship analysis, the panel could effectively distinguish between parent-child, full-sibling, half-sibling, grandfather-grandson, aunt-nephew and unrelated individuals, but uncertainty rates clearly increased when distinguishing between first cousins and unrelated individuals. For the mixtures, the novel panel had demonstrated excellent performance in estimating the number of contributors of mixtures with 1 to 5 contributors in combination with the machine learning methods.ConclusionsIn summary, we have developed a small and high-efficient panel for forensic genetics, which could provide novel insights into forensic complex kinships testing and mixture deconvolution.

Genetic structure of cattle of the siberian branch by microsatellite loci

Molecular-genetic methods are essential tools for the utilization and conservation of animal genetic resources. These methods facilitate more efficient management and control of breeding programs within livestock production systems. For studying the genetic diversity of a population, the use of STR markers is relevant due to the high variability of repeats. This study presents a genetic characterization of a Holstein and Black Pied cattle population (n = 10233) in Western Siberia using 12 microsatellite loci (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53). A total of 145 alleles were identified across all loci, with frequencies ranging from 0.00005 to 0.68961. The highest level of genetic diversity was observed at the TGLA122 locus (25 alleles) with an average number of effective alleles (Ne) of 4.5. The least polymorphic locus was BM1824 (7 alleles) with an average Ne of 3.27. The average observed (Ho) and expected (He) heterozygosity across all loci was 0.6. The highest variability was observed at the TGLA53 locus, with a Wright’s fixation index (Fis) of 0.161, indicating a heterozygote deficiency. A similar deficiency was observed at the BM1818 locus. All other loci exhibited a positive Fis, with the highest value observed at the ETH3 locus (-0.074), indicating an excess of heterozygotes. The average Fis across all loci was -0.02, suggesting a sufficient level of heterozygosity within the studied population. These findings provide valuable information for population studies and practical breeding programs aiming to manage genetic diversity and improve selection efficiency in this cattle population.

Genetic diversity and origin of Kazakh Tobet Dogs

The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level.

Genetic Diversity of Tulipa alberti and T. greigii Populations from Kazakhstan Based on Application of Expressed Sequence Tag Simple Sequence Repeat Markers.

The genus Tulipa L., renowned for its ornamental and ecological significance, encompasses a diversity of species primarily concentrated in the Tian Shan and Pamir-Alay Mountain ranges. With its varied landscapes, Kazakhstan harbors 42 Tulipa species, including the endangered Tulipa alberti Regel and Tulipa greigii Regel, which are critical for biodiversity yet face significant threats from human activities. This study aimed to assess these two species' genetic diversity and population structure using 15 expressed sequence tag simple sequence repeat (EST-SSR) markers. Leaf samples from 423 individuals across 23 natural populations, including 11 populations of T. alberti and 12 populations of T. greigii, were collected and genetically characterized using EST-SSR markers. The results revealed relatively high levels of genetic variation in T. greigii compared to T. alberti. The average number of alleles per locus was 1.9 for T. alberti and 2.8 for T. greigii. AMOVA indicated substantial genetic variation within populations (75% for T. alberti and 77% for T. greigii). The Bayesian analysis of the population structure of the two species indicated an optimal value of K = 3 for both species, splitting all sampled populations into three distinct genetic clusters. Populations with the highest level of genetic diversity were identified in both species. The results underscore the importance of conserving the genetic diversity of Tulipa populations, which can help develop strategies for their preservation in stressed ecological conditions.

Exploring Sampling Strategies and Genetic Diversity Analysis of Red Beet Germplasm Resources Using SSR Markers

By using 14 SSR primer pairs, we here analyzed and compared the amplification results of 534 DNA samples from six red sugar beet germplasm resources under three treatments. These data were used to explore the sampling strategy for the aforementioned resources. Based on the sampling strategy results, 21 SSR primer pairs were used to evaluate the genetic diversity of 47 red sugar beet germplasm resources. The six population genetic parameters used for exploring the sampling strategy unveiled that individual plants within the population had a relatively large genetic distance. The genetic parameters Ne, I, and Nei’s of the randomly mixed sampling samples increased rapidly between 10 and 30 plants before decreasing. Therefore, when SSR technology was used to analyze the genetic diversity of the red sugar beet germplasm resources, the optimal sampling gradient for each population was the adoption of a random single-plant mixed sampling sample of no less than 10 plants and no more than 30 plants. The 21 SSR primer pairs were used to detect genetic diversity in 30 random mixed samples of 47 resources. The average polymorphic information content (PIC) was 0.5738, the average number of observed alleles (Na) was 4.1905, the average number of effective alleles (Ne) was 2.8962, the average Shannon’s information index (I) was 1.1299, the average expected heterozygosity (Nei’s) was 0.6127, and the average expected heterozygosity (He) was 0.6127. The genetic distance of the 47 germplasm resources ranged from 0.0225 to 0.551 (average: 0.316). According to the population structure analysis, the most suitable K value was six, which indicated the presence of six populations. Based on the clustering analysis results, the 47 germplasm resources were segregated into six groups, with obvious clustering and some germplasm resources noted for having groups with close genetic relationships. We here established a more accurate and scientific sampling strategy for analyzing the genetic diversity of red sugar beet germplasm resources by using SSR molecular markers. The findings provide a reference for collecting and preserving red sugar beet germplasms and protecting their genetic diversity.

Genome-wide identification of SSR markers for Curcuma alismatifolia Gagnep., and their potential for wider application in this genus

The genus Curcuma, containing over 120 species, have considerable ornamental, edible and medicinal value. Due to the persistent lack of efficient genomic SSR markers, the conservation and identification of Curcuma genetic resources have faced substantial challenges in practical applications. To date, there are few systematic researches on whole-genome mining of SSR locus in the genus Curcuma. Herein, we performed the first deep identification of genome-wide SSR markers based on the whole-genome data of C. alismatifolia. A total of 257,032 SSR loci were identified with an average density of 216.1–367.3 SSRs/Mb within each chromosome. Mononucleotide repeat loci were most abundant, accounting for 55.1 % of all SSRs, with dinucleotide and trinucleotide repeats accounting for 22.6 % and 20.3 %, respectively. Moreover, 38 polymorphic genomic SSRs (g-SSR) were screened from the synthesized 280 primer pairs, with an average allele number (Na) and polymorphic information content (PIC) of 15.342 and 0.775 per locus, respectively. These markers had excellent cross-species transferability with an overall efficiency of 97.5 % in 21 Curcuma species. According to the cluster and structure analyses, the 178 Curcuma accessions were devided into three major clades correspongding to their origins, hybrid affinities and use values. Finally, a total of 66 Curcuma core collections were preserved, with no significant difference in genetic diversity between the core and entire collections by the t-test. A combination of numbers and letters was employed to establish DNA barcodes for 66 core collections. This study provides valuable molecular markers for wild-collection and conservation, genetic diversity analysis and marker-assisted selection breeding of Curcuma.

Inter and intra population genetic variability in ducks under conservation programs

This study focuses on estimation of the inter and intra population genetic variability of 6 duck populations. Microsatellite loci were used to assess the genetic variation and population structure of 6 duck populations under a conservation program in Poland. DNA polymorphism was assessed using 24 microsatellite markers and 50 individuals from each population. Polymorphism information content (PIC), heterozygosity with 2 estimators of genetic differentiation (FST and GST), and Nei's standard genetic distance were calculated. The results showed that these 6 endangered duck populations showed high genetic polymorphism. Observed heterozygosity within populations ranged from 0.14 to 0.83, with the average value of 0.58. PIC within populations ranged from 0.038 (P-8 and P-9 lines) to 0.89 (LsA line). Average number of alleles in the studied populations ranged from 4.5 (KhO-1 line) to 7.3 (LsA line). Based on the results, the pairs of lines LsA: P-33 and P-8: P-9 were found to be the most related; and the most genetically distant group was KhO-1 line, which originated as a cross between Khaki Campbell with Orpington duck.

Hemoglobin polymorphism and its association with morphometric and egg production traits in Ethiopian indigenous and Sasso chicken breeds.

The present study investigated the biochemical polymorphism of hemoglobin (Hb) and its relationship with performance traits of Ethiopian indigenous and Sasso chicken breeds. A total of 284 chickens reared in three agro-ecologies were examined for genetic diversity and associations with productive traits at Hb locus using agarose gel electrophoresis. The results showed that the HbA allele was dominant in both breeds, and a higher proportion of male chickens were HbAA genotypes, while females were predominantly HbBB types. In the highland agro-ecology, chickens with the HbAA genotype were the most dominant, whereas in mid- and low-land agro-ecologies, chickens with HbBB and HbAB genotypes were found to be more frequent. A moderate level of expected heterozygosity was obtained with 0.47 and 0.445 for indigenous and Sasso chickens, respectively, with an average effective number of alleles per locus of 1.89 and 1.80. Moreover, chickens with HbAA genotypes showed significantly (p ≤ 0.05) higher body weight and linear body measurements than those of HbAB and HbBB genotypes. However, for appendage body structures (comb and wattle dimensions), chickens with the HbAB and HbBB genotypes had higher mean values. Additionally, clutch size (14.2 ± 0.4), clutch length (21.8 ± 0.7), and eight-month egg production (84.1 ± 1.2) were significantly (p ≤ 0.05) higher for hens with HbBB genotypes, followed by those with HbAB-types. Therefore, the considerable hemoglobin variability and significant associations of Hb variants with the performance traits can be sought as guiding information for further genetic improvement interventions in the chicken breeds under investigation. Further microsatellite marker-based genotyping is recommended to validate the higher morphometric values for HbAA genotypes and the better egg production for HbBB and HbAB genotypes.

Genetic and morphological diversity of introduced cultivars of almonds (Prunus amygdalus L.) in Bosnia and Herzegovina.

The main morphological and genetic characterization of seven introduced almond cultivars in Bosnia & Herzegovina was conducted. The almond cultivars included three from Italy (Tuono, Genco, Supernova), two from France (Ferragnes and Ferraduel), and two from the USA (Texas and Nonpareil). Genetic characterization was utilized by using 10 microsatellite markers, with nine markers from Prunus persicae and one from Prunus armeniaca. The results of genetic characterization revealed an average of 5.40 alleles per primer per locus. The average number of effective alleles for the 10 SSR loci of introduced cultivars was 3.92. The Shannon Information Index averaged 1.41. The observed heterozygosity (Ho) and expected heterozygosity (He) averaged 0.53 and 0.69, respectively. Morphological analyses of the fruit of introduced almond cultivars in Bosnia & Herzegovina indicated favorable agroecological conditions for their cultivation and spread. The results suggest that these introduced almond cultivars could be utilized in breeding programs to enhance the genetic diversity of the local almond population in Bosnia & Herzegovina.

Assessment of the genetic similarity between the novoaltayskaya horse breed and the original breeds by microsatellite DNA loci

The research was carried out for the purpose of a comparative assessment of the allele pool of the Novoaltayskaya horse breed and the breeds that participated in its creation. The experimental sample included 5736 horses, including: Novoaltayskaya breed – 363, Altai – 39, Lithuanian Heavy Draft – 159, Russian Heavy Draft – 617, Soviet d Heavy Draft – 288, Orlov trotter – 4,177, Budenny – 93. Population genetic analysis was performed using generally accepted methods. The following indicators were determined: the total number of alleles at 17 loci, the average number of alleles per locus, the level of polymorphism, observed and expected heterozygosity, coefficients of intrapopulation inbreeding, genetic similarity and genetic distances. It was established that horses of the Novo-Altai breed had the highest level of genetic diversity (154 alleles) and polymorphism (Ae = 4,909). Analysis of genetic differentiation showed the absence of intrapopulation inbreeding in the groups of Altai, Lithuanian Heavy Draft and Budenny breeds. Groups of horses of the Novoaltayskaya, Orlov trotter, Russian Heavy Draft and Soviet Heavy Draft breeds were distinguished by a slight deficiency of heterozygotes. It has been established that horses of the Novoaltayskaya and Heavy Draft breeds are characterized by a high frequency of occurrence of the HTG6 O allele, and the Altai breed is characterized by a high frequency of occurrence of the HTG4 M allele. A number of loci of alleles identical in spectrum to those of the Altai, Russian Heavy Draft and Soviet Heavy Draft breeds were identified in the Novoaltayskaya horse. Cluster analysis demonstrated a high level of genetic similarity of horses of the Novoaltayskaya breed with the Russian Heavy Draft (0,903) and Altai (0,899) breeds. As part of the study, using molecular genetic markers, new data was obtained on horses of seven breeds, with the help of which it is possible to improve breeding programs in horse breeding, allowing to control the biodiversity and genetic similarity of populations, preserving the originality and heterogeneity of the allele pool of horses of different breeds.

Simple sequence repeat genotyping of Colletotrichum species associated with soybean anthracnose in Uttarakhand and other states of India

AbstractAnthracnose is one of the most devastating diseases affecting soybean (Glycine max L. Merril) in India and is incited by the Colletotrichum truncatum species complex. In this study, 33 isolates of Colletotrichum spp. isolates were collected from major soybean‐growing states of India. The cultural, morphological and molecular characteristics (Internal Transcribed Spacer rDNA region) of all isolates were demonstrated. Twelve simple sequence repeat (SSR) markers were selected to amplify the genomic DNA of all isolates, to assess the genetic diversity. On the basis of morpho‐cultural and molecular characterization of three different Colletotrichum species, C. truncatum, C. cliviicola and C. cholorophyti were identified. Representative Colletotrichum isolates (Ct‐Pant, Ct‐Gur and Ct‐Gag) from each species group were found pathogenic to susceptible soybean variety (PS 1092) and fulfilled Koch's postulates. The SSR genotyping of 33 isolates revealed that all examined SSR markers exhibited a high degree of polymorphism, as indicated by the mean values of 0.51 for polymorphic information content, 1.97 for marker index and 1.99 for resolving power. For each primer, the average number of alleles per locus was 3.58. The results of Jaccard similarity coefficient‐based UPGMA (Un‐weighted Pair‐Group Method with Arithmetic Mean) cluster analysis and principal component analysis showed that isolates of the same species were clustered together, but no clear‐cut grouping was obtained on the basis of geographical distribution. Thus, it can be inferred from the study that C. truncatum accessions obtained from various geographical locations of India exhibit substantial genetic variation and a significant level of relatedness.

Genetic diversity of a Phascolosoma esculenta population following stock enhancement in Yueqing Bay, East China Sea

Responsible stock enhancement should aim to restore a population while ensuring uninterrupted genetic characteristics of the species. In this study, five pairs of screened microsatellite primers were used to analyze genetic diversity in a wild population (YS, before release), released population (FL), and recaptured population (HB, after release) of Phascolosoma esculenta to assess the impact of stock enhancement in Yueqing Bay. Microsatellite analysis revealed that the average numbers of alleles (Na) for the YS, FL, and HB of P. esculenta were 4.40, 5.40, and 5.40, respectively. The average effective numbers of alleles (Ne) were 2.11, 2.07, and 2.24, respectively. The average observed heterozygosity (Ho) was 0.312, 0.340, and 0.305, respectively, while the average expected heterozygosity (He) was 0.489, 0.465, and 0.496, respectively. The average polymorphic information content (PIC) was 0.425, 0.409, and 0.434, respectively. Analysis of Molecular Variance (AMOVA) revealed that most of the genetic variation was within populations. The genetic differentiation index (FST) values between the three populations were all less than 0.05. The three populations of P. esculenta all had moderate genetic diversity and there was minimal genetic differentiation between the populations, suggesting that the released P. esculenta were suitable for stock enhancement and that the current stock enhancement practices in Yueqing Bay have had no negative impact on the genetic diversity of P. esculenta.

Microsatellite analysis of genetic diversity and population differentiation of Acanthopagrus schlegelii in China

The study utilized 9 self-selected polymorphic microsatellite loci to amplify and investigate the genetic diversity and differentiation of Acanthopagrus schlegelii populations in 10 wild populations along the Chinese coast. The values of Polymorphic Information Content (PIC) ranged from 0.4433 to 0.5804, with an average value of 0.5143. The average number of alleles per locus (A) ranged from 3.0000 to 3.4444, with a mean value of 3.2333 and an overall value of 3.6667. The average number of effective alleles per locus (Ae) ranged from 2.0130 to 2.6014, with a mean value of 2.2994 and an overall value of 2.8013. The observed heterozygosity (Ho) ranged from 0.4607 to 0.5789, with an average value of 0.5278 and an overall value of 0.5261. The expected heterozygosity (He) ranged from 0.4657 to 0.5967, with an average value of 0.5183 and an overall value of 0.6224. The results of genetic differentiation showed the genetic differentiation coefficient (Fst) was 0.1806, and the gene flow (Nm) was 1.1342. The UPGMA cluster analysis indicated significant genetic differentiation among A. schlegelii populations along the Chinese coast, with the populations being divided into two groups, namely the northern and southern populations. The genetic differentiation structure of the southern population was inconsistent with its geographical distribution. This study utilized microsatellite molecular markers to investigate the genetic diversity and genetic differentiation of 10 wild A. schlegelii populations along the coast of China. The research results indicate that the genetic diversity of the 10 wild A. schlegelii populations is at a moderate level, with evidence of north-south differentiation. This provides a scientific basis for the conservation, germplasm improvement, and aquaculture of A. schlegelii resources in China. It also offers background information for recent stock enhancement and release projects and their impact on the genetic resources of A. schlegelii.

Genetic Diversity and Construction of Core Collection of Sterculia Germplasm

Amplification of 107 Sterculia accessions with 12 ISSR primers resulted in 235 bands, the percentage of polymorphic sites was 100%, with the average number of effective alleles (Ne) of 1.2464, the average Nei’s gene diversity index (H) of 0.1556, the average Shannon's information index (I) of 0.2563, and the average polymorphism information content (PIC) of 0.8594, indicating that the collected 107 accessions had high genetic diversity. The genetic diversity was unevenly distributed among Sterculia samples collected from different provinces, and the highest value was observed in samples from Guangdong Province, followed by those from Yunnan Province, and the lowest was from Guangxi Province. The core collection construction of the 107 Sterculia accessions was carried out by using the SCR and LDSS methods, respectively, and the results showed that the LDSS method was more suitable for Sterculia germplasm. Different core collections were constructed based on sampling proportions of 35, 30, 25, 20 and 15%, respectively, the t-test and principal coordinates analysis results showed that the genetic diversity of the original germplasm can be fully represented at a sampling proportion of 30%. Bangladesh J. Bot. 53(2): 319-325, 2024 (June)

Genetic diversity of the critically endangered Blue‐crowned laughingthrush (Garrulax courtoisi)

AbstractTo evaluate the genetic quality and provide available management strategies for Blue‐crowned laughingthrush (BCLT), fifteen polymorphic microsatellite loci were developed and applied. The genetic diversity of wild individuals was indicated to be higher than the two captive populations. The average number of alleles (5.50 ± 0.317), the number of effective alleles (3.417 ± 0.222), observed heterozygosity (0.828 ± 0.04), and genetic differentiation index (0.028 ± 0.007) of 64 wild individuals showed high genetic diversity despite drastic bottleneck and low genetic differentiation. The number of effective migrants (22.737 ± 8.318) indicated the intriguing wintering grounds may be surrounded by the breeding sites where the syncheimadia occurred in Wuyuan. Efficient conservation, winter flocking, and cooperative breeding may facilitate gene exchange and inclusive fitness. We recommend that monitoring concentrated distribution areas for BCLT should be strengthened, and geographical barriers, interference types, and the inner mechanism of distribution patterns should be further explored.

Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils.

The Mongolian gerbil is a distinctive experimental animal in China, as its genetic qualities possess significant value in the field of medical biology research. Here, we aimed to establish an economical and efficient panel for genetic quality detection in Mongolian gerbils using single-nucleotide polymorphism (SNP) markers. To search for SNPs, we conducted whole-genome sequencing (WGS) in 40 Mongolian gerbils from outbred populations. Reliable screening criteria were established to preliminarily select SNPs with a wide genome distribution and high levels of polymorphism. Subsequently, a multiple-target regional capture detection system based on second-generation sequencing was developed for SNP genotyping. Based on the results of WGS, 219 SNPs were preliminarily selected, and they were established and optimized in a multiple-amplification system that included 206 SNP loci by genotyping three outbred populations. PopGen.32 analysis revealed that the average effective allele number, Shannon index, observed heterozygosity, expected heterozygosity, average heterozygosity, polymorphism information content, and other population genetic parameters of the Capital Medical University (CMU) gerbils were the highest, followed by those of Zhejiang gerbils and Dalian gerbils. Through scientific screening and optimization, we successfully established a novel, robust, and cost-effective genetic detection system for Mongolian gerbils by utilizing SNP markers for the first time.

Genetic Diversity Assessment of Cupressus gigantea W. C. Cheng & L. K. Fu Using Inter-Simple Sequence Repeat Technique

Cupressus gigantea W. C. Cheng & L. K. Fu is an endemic conifer tree species that is distributed widely along the northern portion of the deep gorge of the Yarlung Tsangbo River on the Tibetan Plateau. However, as a key plant species growing on the Tibetan plateau, C. gigantea has since become an endangered species due to habitat loss and degradation, overexploitation, and other factors. It has been listed as a first-grade national protected wild plant species in China. Accordingly, to conserve this plant species, we should obtain more information on its genetic structure. In this study, the genetic diversity and structure among 67 samples were evaluated by the inter-simple sequence repeat (ISSR) technique. Overall, 78 bands were produced with a molecular length of 200 bp to 3100 bp using 10 ISSR primers. The mean values for the average number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity (H), and Shannon’s information index (I) were 1.529, 1.348, 0.199, and 0.293, respectively. Additionally, the number of polymorphic loci (NPLs) and percentage of polymorphic loci (PPLs) averaged 41.25 and 52.90, respectively. Further, total variation among populations was 14.2%, while that within populations was 85.8%; accordingly, the within-population genetic differentiation was found to be significant (p < 0.001). These results demonstrated that a genetic structure model with K = 3 fitted the data best, which agreed with the unweighted pair group method with arithmetic average (UPGMA) cluster and the principal coordinate analysis (PCoA). These findings are beneficial for ensuring the development and genetic protection of C. gigantea populations in the future.

Microsatellite marker-based analysis of the genetic diversity and population structure of three Arnebiae Radix in western China

Arnebiae Radix is an important medicinal and perennial herb found in Western China, particularly in the Xinjiang region. However, the assessment, utilization and conservation of Arnebiae Radix resources are still unexplored. In this study, we evaluated the genetic diversity of three Arnebiae Radix populations across 47 regions (Ae = 16, Ag = 16, Ad = 15) in Xinjiang, China, using inter-simple sequence repeat (ISSR) molecular markers. In total, 48 alleles were amplified by six pairs of primers screened with ISSR markers. The average number of effective alleles (Ne) was 1.5770. The percentage of interspecific genetic polymorphisms in A. guttata (Ag = 89.58 %) was greater than that in A. euchroma. and A. decumbens (Ae = Ad = 87.50 %). Intraspecific genetic polymorphisms, Bo Le (BL) population of A. euchroma exhibited the highest percentage of polymorphic bands (PPB% =58.33 %, Na = 1.313, Ne = 1.467, I = 0.0.366, H = 0.255), which indicated high genetic diversity. In contrast, the Tuo Li (TL) population of A. guttata had the lowest values for these parameters (PPB% =0.00 %, Na = 0.313, Ne = 1,000, I = 0.000, H = 0.000). The Arnebiae Radix germplasms were classified into two major groups (I and II) based on UPGMA cluster analysis (Fig. 8a) and principal coordinate analysis (PCOA). In addition, A. decumbens is placed in a separate category due to its high differentiation coefficient. The AMOVA and genetic differentiation coefficient results indicated that the genetic variation in Arnebiae Radix was predominantly due to intrapopulation differences (78 %). Additionally, the gene flow index (Nm) between populations was 2.4128, which further indicated that the genetic diversity of Arnebiae Radix was greater at the intrapopulation level. The destruction of the ecological environment leads to the continuous reduction and degradation of the genetic diversity of Arnebiae Radix germplasm resources. In this study, we used ISSR molecular markers to analyze the genetic diversity and relatedness of Arnebiae Radix, which revealed the genetic relationship of Arnebiae Radix germplasm resources at the molecular level and provided a scientific basis for future research on selecting and breeding good varieties, evaluating the quality of Arnebiae Radix, and conserving and utilizing its resources.

Construction of a DNA Fingerprint Map and a Core Collection of Platycladus orientalis

Platycladus orientalis is one of the main species used in afforestation projects in the arid mountains of north and northwest China, meaning that the species has high ecological and economic value. Studying its genetic diversity and obtaining a core germplasm base and genetic fingerprint data are important for the screening, development, and utilization of the species. This can provide the core materials for the preservation and evaluation and mining of germplasm resources and can provide superior gene resources for breeding programs. In this study, the genetic diversity among 104 P. orientalis germplasm resources was examined using simple sequence repeat (SSR) markers, and a core germplasm containing 31 accessions was constructed that represents the most genetic diversity of P. orientalis accessions. Each of 20 pairs of primers showed polymorphism, and 117 alleles were identified. The average number of alleles at each locus was six, and the mean effective allele number was 2.607. The average Shannon’s information index was 0.983, and the average polymorphism information content was 0.445. There is thus a significant amount of genetic variation within P. orientalis germplasm, yielding a rich genetic diversity. The constructed core germplasm accounted for 30% of the original germplasm. There was no significant difference in genetic diversity between the core germplasm and the original germplasm resources, indicating that the obtained core germplasm resources could fully represent the original germplasm. Using 17 SSR primers with high polymorphism, the DNA fingerprints of 104 P. orientalis germplasm resources were constructed. The results showed that 98 had specific DNA fingerprints. The results of this study provide a valuable basis for the collection, preservation, and utilization of P. orientalis germplasm resources, and the methods adopted in this study have important reference value for the construction of core germplasm of other perennial woody plants.